Re: [Fis] Are there 3 kinds of motions in physics and biology?

2018-05-07 Thread Michel Petitjean
Dear Karl,
Yes I can hear you.
About symmetry, I shall soon send you an explaining email, privately,
because I do not want to bother the FISers with long explanations
(unless I am required to do it).
However, I confess that many posts that I receive from the FIS list
are very hard to read, and often I do not understand their deep
content :)
In fact, that should not be shocking: few people are able to read
texts from very diverse fields (as it occurs in the FIS forum), and I
am not one of them.
Even the post of Sung was unclear for me, and it is exactly why I
asked him questions, but only on the points that I may have a chance
to understand (may be).
Best regards,

2018-05-07 17:55 GMT+02:00 Karl Javorszky :
> Dear Michel and Sung,
> Your discussion is way above my head in the jargon and background knowledge.
> Please bear with me while a non-mathematician tries to express some 
> observations that regard symmetry.
> Two almost symmetrical spaces appear as Gestalts, expressed by numbers, if 
> one orders and reorders the expression a+b=c. One uses natural numbers – in 
> the range of 1..16 – to create a demo collection, which one then sorts and 
> re-sorts ad libitum / ad nauseam. The setup of the whole exercise does not 
> take longer than 1, max 2 hours. Then one can observe patterns.
> The patterns here specifically referred to are two – almost – symmetrical 
> rectangular, orthogonal spaces. As these patterns are derived from simple 
> sorting operations on natural numbers, one can well argue that they represent 
> fundamental pictures.
> The generating algorithm is 5 lines of code. Here it is.
> #d=16
> begin outer loop, i:1,d
> begin inner loop, j:i,d
> append new record
> write
>  a=i, b=j, c=a+b, k=b-2a, u=b-a, t=2b-3a,
> q=a-2b, s=(d+1)-(a+b), w=2a-3b
> end inner loop
> end outer loop

> The next step is to sequence (sort, order) the rows. We use 2 sorting 
> criteria: as first, any one of {a,b,c,k,u,t,q,s,w}, and as 2nd sorting 
> criterium any of the remaining 8. This makes each of the 9 aspects of a+b=c 
> to be once a first, and once a second sorting key. We register the linear 
> sequential number of each element in a column for each of the 72 catalogued 
> sorting orders..
> Do you think the idea of symmetry is somehow connected to some very basic 
> truths of logic? Then maybe the small effort to create a database with 136 
> rows and 9+72 columns is possible.
> The trick begins with the next step:
> We go through the 72 sorting orders and re-sort from each of them into all 
> and each of the remaining 71. We register the sequential place of the element 
> in the order αβ while being resorted into order γδ. This gives each element a 
> value (a linear place, 1..136) “from” and a value “to”. The element is given 
> the attributes: Element: a,b, “Old Order”: αβ, from place nr i, “New Order” 
> γδ, to place nr. j. While doing this, one will realise, that reorganisations 
> happen by means of cycles, and will add attributes :
> Cycle nr: k, Within cycle step nr:. l. This is simple counting and using 
> logical flags.
> The cycles, that we have now arrived at, give a very useful skeleton for any 
> and all theories about order. You will find the two Euclid-type spaces by 
> filtering out those reorganisations that consist of 46 cycles, of which 45 
> have 3 elements in their corpus, where each of the 45 cycles has Σa=18, Σb=33.
> The two rectangular spaces – created by paths of elements during resorting – 
> are not quite symmetrical. As an outsider, I’d believe that there is 
> something to awake the natural curiosity of mathematicians.
> Hoping to have caught your interest.
> Karl

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Re: [Fis] Are there 3 kinds of motions in physics and biology?

2018-05-07 Thread Michel Petitjean
Dear Sung,

The formula of the Planckian information in Table 1 is intriguing.
The argument of the log_2 function was proposed in 1895 by Karl Pearson as
a measure of asymmetry of a distribution (see [1], p. 370).
In general the mean can be smaller than the mode (so the log cannot exist),
but I assume that in your context that cannot happen.
Also, I assume that this context excludes distributions such as a mixture
of two well separated unit variance Gaussian laws, for which the mean is
located at an antimode, and not at a mode.

The skewness, which is also used as an asymmetry coefficient, is the
reduced third order centered moment (may be positive or negative).
The square of this latter quantity was also introduced by Karl Pearson as a
measure of asymmetry of a distribution (see [1], p. 351).

So, all these quantities are used as asymmetry measures.

Two questions arise:
1. Has the Planckian information some relations with symmetry or asymmetry?
If yes, which ones?
That would not be shocking: Shu-Kun Lin (refs [2,3]) discussed about
relations between information and symmetry.
2. The asymmetry measures above have a major drawback: a null value can be
observed for some families of asymmetric distributions, and not only for
symmetric distributions.

In the case you indeed need to consider the log of a non negative quantity
measuring the asymmetry of a distribution, which vanishes if and only if
the distribution is symmetric, you may consider the chiral index \chi
(section 2.9, ref [4]).
\chi index takes values in [0..1] (in fact, in [0..1/2]) for univariate
probability distributions, and it is null if and only if the distribution
is symmetric.
It has other properties, but that falls out of the scope of this discussion.
Then, simply replace [ (\mu-mode) / \sigma ] by \chi as the argument of

[1] Pearson, K.
Contributions to the Mathematical Theory of Evolution,-II. Skew Variation
in Homogeneous Material.
Phil. Trans. Roy. Soc. London (A.), 1895, 186, 343-414.

[2] Lin, S.K.
Correlation of Entropy with Similarity and Symmetry.
J. Chem. Inf. Comput. Sci. 1996, 36, 367--376

[3] Lin, S.K.
The Nature of the Chemical Process. 1. Symmetry Evolution –Revised
Information Theory, Similarity Principle and Ugly Symmetry.
Int. J. Mol. Sci. 2001, 2, 10--39
(available in open access)

[4] Petitjean, M.
Chirality and Symmetry Measures: A Transdisciplinary Review.
Entropy, 2003, 5[3], 271--312.
(available in open access)

Best regards,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

2018-05-07 4:08 GMT+02:00 Sungchul Ji <>:

> Hi FISers,
> I think information and energy are inseparable in reality.  Hence to
> understand what information is, it may be helpful to understand what energy
> (and the associated concept of motion) is.  In this spirit, I am forwarding
> the following email that I wrote motivated by the lecture given by Dr.
> Grossberg this afternoon at the 119th Statistical Mechanics Conference.  In 
> *Table
> 1* in the email, I divided particle motions studied in physics and
> biology into three classes -- (i) *random*, (ii) *passive*, and (iii)
> *active*, and identified the field of specialization wherein these
> motions are studied as (i) *statistical mechanics*, (ii) *stochastic
> mechanics*, and (iii) *info-statistical mechanics*.  The last term was
> coined by me in 2012  in [1].  I will be presenting a short talk (5
> minutes) on* Info-statistical mechanics* on Wednesday, May 9, at the
> above meeting.   The abstract of the short talk is given below:
> Short talk to be presented at the *119th Statistical Mechanics Conference*,
> Rutgers University, Piscataway, N.J., May 6-9, 2018).
> *Planckian Information** may be to Info-Statistical Mechanics what
> Boltzmann Entropy is to Statistical Mechanics. *
> Sungchul Ji, Department of Pharmacology and Toxicology, Ernest Mario
> School of Pharmacy, Rutgers University, Piscataway, N.J. 08854
> Traditionally, the dynamics of any N-particle systems in statistical
> mechanics is completely described in terms of the 6-dimensional *phase
> space* consisting of the 3N positional coordinates and 3N momenta, where
> N is the number of particles in the system [1]. Unlike the particles dealt
> with in statistical mechanics which are featureless and shapeless, the
> particles in biology have characteristic shapes and internal structures
> that determine their biological properties.  The particles in physics are
> completely described in terms of energy and matter in the phase space but
> the description of the particles in liv

Re: [Fis] Welcome to Knowledge Market and the FIS Sci-coins

2018-03-22 Thread Michel Petitjean
Dear Arturo,
Sorry for my naive question, but isn't the named set theory something
different from the set theory?

2018-03-22 7:48 GMT+01:00 :
> Dear Mark,
> the named set theory does not solve the Russell paradox.
> Therefore  it would be better to use, in such approaches, the best theory 
> available, i.e., the Fraenkel-Zermelo sets.
> In turn, the latter displays some limits: for example, the need of a set with 
> infinite elements.
> Therefore, set theory is not able to tackle information problems.
> You have to go back to other mathematical approaches.

 . . .

> Arturo Tozzi
> AA Professor Physics, University North Texas
> Pediatrician ASL Na2Nord, Italy
> Comput Intell Lab, University Manitoba
> ___
> Fis mailing list
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Re: [Fis] I do not understand some strange claims

2017-11-09 Thread Michel Petitjean
Dear Arturo,

I share most of your views below.
However, I would not systematically reject the contributions of
philosophers in information science (and in general), even if some of
them are unreliable.
But what could be a world without philosophers?
And are we ourselves so reliable?
In fact, your opinion below surprised me, particularly after having
looked at your web site, where it is possible to read several papers
you wrote (in various journals, in viXra, etc), including the short
manuscript that summarizes your scientific results:
Anybody can read it (3 text pages + 2 pages of refs).
Yes there are pseudo-sciences all around the world, and they should be
I like to do that, sometimes...

Best regards,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

2017-11-08 22:11 GMT+01:00 <>:
> Dear FISers,
> science talks about observables, i.e., quantifiable parameters.
> Therefore, describing the word "information" in terms of philosophers' 
> statements, hypothetical useless triads coming from nowhere, the ridicolous 
> Rupert Sheldrake's account, mind communication, qualitative subjective issues 
> of the mind, inconclusive phenomelogical accounts with an hint of useless 
> husserlian claims, and such kind of amenities is simply: NOT scientific.
> It could be interesting, if you are a magician or a follower of Ermetes 
> Trismegistus, but, if you are (or you think to be) a  scientist, this is 
> simply not science.
> Such claims are dangerous, because they are the kind of claims that lead to 
> NO-VAX movements, religious stuff in theoretical physics, Heideggerian 
> metapyhsics.  Very interesting, but NOT science.
> That's all: 'nuff said.
> Arturo Tozzi
> AA Professor Physics, University North Texas
> Pediatrician ASL Na2Nord, Italy
> Comput Intell Lab, University Manitoba

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Re: [Fis] mind-mind

2017-11-01 Thread Michel Petitjean
Dear Krassimir, dear ALex, dear All,

I agree with Krassimir that ideas cannot be transmitted directly from
Mind to Mind.
Being a materialist, I consider that only matter exists.
Does it mean that information is matter or energy?
Let me discuss about this contradiction.
Parenthesis: energy is linked to mass through math modeling of
physical laws, and mass is a property of matter (could also be linked
to a modeling concept, but it is unimportant here).
People (not only scientists) build math and non math models to attempt
to explain what they observe.
Would you consider that math is matter?
Probably no.
Thus math and non math models that we build in our heads are not matter.
However they are produced through some biochemical process, and as
such they originate from matter.
Eventually, it could be considered that math and other concepts are a
somewhat special part of matter, but I think that claim would not be
accepted in our current language(s).
I consider that "soul", "god", and some other concepts are built in our heads.
In my opinion, these concepts at best incoherent, if not worse.
Remark: I have nothing against religions, as far as believers do not
impose to me the consequences of their beliefs.
Religious beliefs must be private affairs.
Here, please accept my apologies if some of you are shocked by the
previous sentences.

Information is like math: it is a modeling concept applied to some situations.
However, I do not claim that information can be reduced to the math
concepts of information.

To conclude:

1. I agree with Principle 1 of Pedro.

2. I assume potential contradictions in my views. No problem: I am a
poor philosopher.
Then,I never claimed that I am "built" to be able to elaborate a
coherent theory about life, consciousness , etc. May be it is
impossible. May be that cannot be decided, etc.
All that is opinions. It is just nice and funny to discuss information
and so on.

3. If I would vote for a definition of information, I would retain the
one of Karl.
Citing Karl in his post of the 3 Oct 2017:
"Data is that what we see by using the eyes. Information is that what
we do not see by using the eyes, but we see by using the brain;
because it is the background to that what we see by using the eyes."

All my best,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

> Dear Alex and FIS Colleagues,
> Thank you for the nice remark.
> I had listen about such hypothesis but till now I had no participate in any 
> experiment of transferring ideas mind-mind. Maybe you had taken place in such 
> experiments. Please, give link to publications in scientific issues about 
> this very interesting phenomenon.
> Simple question: If it is possible to transfer ideas mind-mind, why you use 
> FIS List to send your ideas to us?
> Friendly greetings
> Krassimir
> PS: Unfortunately, this is my second post for this week and I please to 
> excuse me for answering the next posts after week.
> From: Alex Hankey
> Sent: Wednesday, November 01, 2017 12:21 PM
> To: Krassimir Markov
> Cc: FIS Webinar
> Subject: Re: [Fis] About 10 Principles
> RE: P1. Information is information, neither matter nor energy.
> M1. Information is a class of reflections in material entities. Not every 
> reflection is information. Only subjectively comprehended reflections are 
> information.
> ME: Ideas can be transmitted directly from Mind to Mind - as in Rupert 
> Sheldrake's 7th Sense Communication.
> Lots of Quantitative Evidence that Materialists Prefer to Ignore.
> The Experience Information model of the Cognitive States shows that such 
> Information States Are Not Material Entities.
> They are based round instabilities in Networks of Neurons.
> The ability to model Seventh Sense Communication means that this phenomenon 
> becomes one of Four Separate Ways to Generate Empirical Evidence in support 
> of them.
> Hence Information is Not Matter or Energy.
> This is but one example of how Principles 1 to 5 can be supported.

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Re: [Fis] Principles of IS

2017-09-30 Thread Michel Petitjean
Dear Arturo, dear FISers,

Citing Beck (Contemp. Phys. 2009, 50, 495–510. doi:
10.1080/00107510902823517), Street wrote: << information can be
defined as a negation of thermodynamic entropy (Beck, 2009): I=-S >>
(pls. read the equal sign with three bars, I don't know how to type
the three bars sign).
But Beck wrote about information theory (i.e. the probabilistic one):
<<  One then defines the entropy S as ‘missing information’, i.e. S=-I
Thus it is not what claimed Street: (i) Beck referred to probability
theory (no thermodynamics there), and (ii) Beck defined S from I, not
I from S.
So the claim of Street is doubtful, if not false.
Bt the way, the Publisher of "Frontiers Systems in Neuroscience" was
classified as predatory in the Beall's list, but let us forget it.

Beck is in agreement to what is told on, << The
inspiration for adopting the word entropy in information theory came
from the close resemblance between Shannon's formula and very similar
known formulae from statistical mechanics. >>
As far as I know, what is related in the Wikipedia page is an historical fact.
Entropy has thus two meanings: a physical quantity in thermodynamics,
and a math quantity in the framework of modeling communication
Information is also a math quantity in the framework of modeling
communication science: it is a modeling concept which is not physical.
Playing again with words, some people introduced the term information
back in thermodynamics, thus concluded that information is physical.
In my opinion it is not a good practice: it adds confusion.

Best regards,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

2017-09-29 14:01 GMT+02:00  <>:
> Dear FISers,
> Hi!
> ...a very hot discussion...
> I think that it is not useful to talk about Aristotle, Plato and Ortega y 
> Gasset, it the modern context of information... their phylosophical, not 
> scientific approach, although marvelous, does not provide insights in a 
> purely scientific issue such the information we are talking about...
> Once and forever, it must be clear that information is a physical quantity.
> Please read (it is not a paper of mine!):
> Street S.  2016.  Neurobiology as information physics.  Frontiers in Systems 
> neuroscience.
> In short, Street shows how information can be clearly defined in terms of 
> Bekenstein entropy!
> Sorry,
> and BW...
> Arturo Tozzi
> AA Professor Physics, University North Texas
> Pediatrician ASL Na2­Nord, Italy
> Comput Intell Lab, University Manitoba
> http://arturotozzi.w­
> -

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2017-09-15 Thread Michel Petitjean
Dear Pedro, dear Arturo and dear FISers,

Thank you Pedro for these 10 principles of information science.
Even if it happens that somebody could disagree with some of these
principles, at least these 10 principles exist and they constitute a
suitable basis (if not a reference) for further discussions and

I agree with the principle 1, in the sense that, in my opinion
information is not physical: it is in our heads, either as a
mathematical model of some physical situation, or as a concept we need
to deal with some real situation.
An observed physical phenomenon should not be confused with any
mathematical model produced by scientists to get a more or less
simplified description of this phenomenon.
E.g., the thermodynamical entropy can be modeled by an equation
formally identical to the well-known one used in communication
Does it mean the informational entropy and the thermodynamical entropy
are the same thing because both lead to a common equation?
I do not believe so: one word, two meanings.
Then, the possibility to measure information in communication science
does not mean that information becomes a physical quantity in other
contexts, such as matter (the case of energy is more complex, I skip
Finally, why not try to define information in metaphysics, sociology
or psychology?
Dictionnaries contain thousands of words defined without the help of
mathematics, and fortunately these definitions are of great help in
most situations.
However, finding a unifying definition of information is still a challenge.
But is it feasible? Is it desirable?
I don't know...

Best regards,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),


Unifying symmetry definition in maths:

Recent highlight: chirality can be defined without the help of any
orientation concept:

Chirality in metric spaces. In memoriam Michel Deza.
Optim. Letters, 2017


2017-09-15 15:16 GMT+02:00 <>:
> Dear FISers,
> I'm sorry for bothering you,
> but I start not to agree from the very first principles.
> The only language able to describe and quantify scientific issues is 
> mathematics.
> Without math, you do not have observables, and information is observable.
> Therefore, information IS energy or matter, and can be examined through 
> entropies (such as., e.g., the Bekenstein-Hawking one).
> And, please, colleagues, do not start to write that information is subjective 
> and it depends on the observer's mind. This issue has been already tackled by 
> the math of physics: science already predicts that information can be 
> "subjective", in the MATHEMATICAL frameworks of both relativity and quantum 
> dynamics' Copenhagen interpretation.
> Therefore, the subjectivity of information is clearly framed in a TOTALLY 
> physical context of matter and energy.
> Sorry for my polemic ideas, but, if you continue to define information on the 
> basis of qualitative (and not quantitative) science, information becomes 
> metaphysics, or sociology, or psychology (i.e., branches with doubtful 
> possibility of achieving knowledge, due to their current lack of math).
> Arturo Tozzi
> AA Professor Physics, University North Texas
> Pediatrician ASL Na2Nord, Italy
> Comput Intell Lab, University Manitoba
> Messaggio originale
> Da: "Pedro C. Marijuan" <>
> Data: 15/09/2017 14.13
> A: "fis"<>
> Dear FIS Colleagues,
> As promised herewith the "10 principles of information science". A couple of 
> previous comments may be in order.
> First, what is in general the role of principles in science? I was motivated 
> by the unfinished work of philosopher Ortega y Gasset, "The idea of principle 
> in Leibniz and the evolution of deductive theory" (posthumously published in 
> 1958). Our tentative information science seems to be very different from 
> other sciences, rather multifarious in appearance and concepts, and 
> cavalierly moving from scale to scale. What could be the specific role of 
> principles herein? Rather than opening homogeneous realms for conceptual 
> development, these information principles would appear as a sort of "portals" 
> that connect with essential topics of other disciplines in the different 
> organization layers, but at the same time they sho

Re: [Fis] Never mind

2016-01-26 Thread Michel Petitjean
Dear Emanuel,

An invitation to submit does not mean that the paper will be published.
Open access (OA) journals publishers send numerous emails to convince
authors to submit.
Sometimes it is done at the occasion of a conference, and it can be even
mentioned on the conference website.
If all the submitted manuscripts would be published, the quality of the OA
journals would be very poor.
This indeed happens for predatory journals and publishers, for which almost
all manuscripts are published provided that the authors pay the page charge.
Fortunately, a serious journal have an editor, and the job of this latter
is to decide if submitted manuscripts should be published or not.
The word "invitation" is also used for conferences.
As for journals, it just means that you are welcome to submit a
contribution, but without any guarantee that it will be accepted (a true
invited contribution is ususally associated to a funding, at least partial).
When a journal paper is invited, in the sense that anyway it will be
published (possibly after corrections), it is explicitely mentioned by the
editor in his invitation letter.
In the case of your paper, I do not see any contradiction between the
invitation and the rejection.

Best regards,

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

2016-01-26 8:12 GMT+01:00 Emanuel Diamant <>:

> Dear Pedro,
> Shortly after the Vienna Summit, I was invited to submit an extended
> version of my conference paper for a publication in the Special Issue of
> the Information journal "Selected Papers from the ISIS Summit Vienna 2015".
> It took me a lot of time to prepare the manuscript, but in the end, it was
> submitted to the journal.
> Soon afterwards, I was informed that “your manuscript has been declined
> for publication in Information”.
> No comments, no further explanations – I have some previous experience
> with publishing selected conference papers in revered journals but that is
> my first encounter with such invited paper treatment style.
> Never mind, I have published the article in the Research Gate. Because its
> subject is closely related to the discussion we held on the FIS forum in
> October 2015, I dare to provide a link to this RG publication (may be the
> issue is still interested for some FIS partakers).
> Best regards,
> Emanuel Diamant.
> ___
> Fis mailing list
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[Fis] Tragedy in USA

2015-12-05 Thread Michel Petitjean
Dear All,

Please let me address my condolences to the families of the victims of
the killing at San Bernardino.

Here follows a list :
(partial; apologies for the forgotten items)

Afghanistan, Australia, Belgium, Cameroon, Denmark, India, Indonesia,
Irak, Egypt, France, Mali, Nigeria, Pakistan, Russia, Spain, Tchad,
Tunisia, UK, USA, ...

Anybody can be victim : young, old, man, woman, christian, muslim,
living in a pacific country or not, ...

Political problems explain few.
Most of that is due to obscurantism, conjugated to the ambition of
some gurus of sects, who do not care about the lives of the victims
and of lives of the mistaken young people serving these gurus.

No progress since the Middle Ages.
No progress since the Antiquity.

Education was efficient for sciences and techniques, but light is
still missing in our poor brains.


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[Fis] Again and again...

2015-11-24 Thread Michel Petitjean
Dear All,
A few days after the attack in Bamako, Tunis is attacked.
Again and again innocent people are killed.
Terrorism never ends.
Let me address my condolences to the families of the victims.
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Re: [Fis] Tragedy in France

2015-11-18 Thread Michel Petitjean
Dear Chuan,

Many thanks for this so wonderful poem !
It is so nice.
It is a masterpiece.

With all my best,


(To Pedro: I'm very grateful to you for having let me to post this
beautiful poem discarding the rules of the Fis list)

2015-11-18 15:51 GMT+01:00 赵川 :
>  The beauty and innocent
> “The beauty and innocent”
> The news of this November of tragedy from Paris
> let me murmured John Lennon’s murmur
> “The beauty and innocent”
> In the theatre, it is the peace place…
> “The beauty and innocent”
> Thou, human being
> Who the beauty and innocent
> Who the evil and conceited
> All should be sober
> Ware, ware and ware
> Archimedes said to the soldier: let me drew this circle round then…
> Yes, Thousands year ago
> There was such a classical scene similar same
> What can I do?
> What can I do?
> Keep awareness only
> Why then…
> No such then…
> In the entrance after the fresh terrible air in silence
> from an serious piano John’s “Imagine” rising
> We should pray for Paris
> And even for Damascus the same
> We should pray for all the world
> Violence can never destroy righteousness
> This even more means that evil aware they are error and go back
>and why righteousness is right and go on
> that should be a save circle
> like arms forming hug
> War is ugly and barbaric is not brave
> Real courage is look inner and watch around and beyond self
> Yes, dear Pedro
> the head of another ISIS
> Your call is right -
> Let us burn words from our heart to shine the dark
> I hear the voice over of a film I read, Joan of Arc
> “It is the darkest time of France”
> for it hurt the heart of France
>  stabbed the spirit of France
> Zhao Chuan 2015-11-18 China

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[Fis] Information and OA

2015-08-31 Thread Michel Petitjean
Subj: Information and OA

Dear All,

Since several months I receive each week a number of emails
sollicitating me to submit papers to OA (Open Access) journals.
Probably many of you receive such emails, too.
I am happy that OA journals exist because they provide a free access
to scientific information all around the world for those accessing to
The counterpart of this free access is that the authors have to pay a
page charge, and this is reasonable because the publishers must earn
money, as for non OA journals.
But while there are several publishers doing a good job, there is an
increasing number of predatory publishers.
I can see that even experienced Academics are unaware of this problem
and it is why I am writing these lines.
A list of predatory publishers was established by the librarian
Jeffrey Beall: see and related
In many cases it can be checked that the content of this list is right
while in some cases it may be discussed.
The quality of a journal does not depend only on the publisher: it
strongly depends on the work of the Editor-in-Chief.
The quality of the journals of a given publisher may greatly vary from
one journal to an other journal.
It can also vary along the time.
Then let me recall that even the most prestigious non OA journals such
as Science or Nature published doubtful papers (e.g. it happened that
papers in Science were retracted).
Conversely, it happened that good papers can be published in
unrecognized journals, and even sometimes in the proceedings of
unimportant conferences.
The extreme case may be arXiv, in which poor papers can be found
together with major quality papers (while unpublished in journals:
e.g. see
Thus, deciding to classify a publisher as predatory or not is
difficult, and the result of this decision can hide a complex reality
that should be examined.
Your opinions are welcome.

Best regards,


Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),
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[Fis] MDA 2012: a great time !

2012-07-10 Thread Michel Petitjean
Subj: MDA 2012: a great time !

Dear All,

The MDA multidisciplinary Conference on Mathematics of Distances and
was held at Varna, July 2-5 2012.

Please have a look at:

Krassimir Markov and the Bulgarian organizing team did a very great job.

Krassimir is an experienced organizer, and I strongly recommend him
for organizing
more Conferences: Varna is a nice place in front of the Black Sea,
which is great
to welcome a FIS Conference.
In addition to the FIS, the FOI Bulgaria has a number of important
connections with
academic organizations, most being related to Information Science and
neighbouring fields.

All my best,


Michel Petitjean,
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),
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Re: [Fis] Chemo-informatics as the source of morphogenesis - both practical and logical.

2011-10-17 Thread Michel Petitjean
Dear Loet and dear Jerry,

2011/10/17 Loet Leydesdorff
 Dear Jerry,
 It may be easiest to raise some questions:

 1. What is the equivalent in chemo-informatics of a bit of information? Can
 this be operationalized as a formula like Shannon's H?
 2. Can one compute with this formula in fields other than chemistry? For
 example, in economics; without using metaphors? (As if)

If (1) can be answered, thus chemoinformation enters in the field of
information theory. That would be a very strong result.
Alas, I am afraid that it can't. Sets of flexible 3D realized graphs
seem hard to give raise ti bits of information.
But I didn't proved that. Who knows, if a good mathematician can
answer to (1), it would be a great advance in the field.
And I did not speak about (2) ...

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-24 Thread Michel Petitjean
Dear FISers,

Many thanks to Xueshan Yan for these three examples of cheminformation.
I agree that among the various cheminformation concepts, some are technological.
E.g., the Infonortics conferences (the 2011 one held in Barcelona:,
are oriented to professional information, rather in the sense of
publishing. That should be of interest for professional information
people in a broader sense, not only in a technology of publication one
and related.
On the other hand, cheminformatics conferences and workshops organized
in various countries, such as in USA (by CINF division of the ACS,
mentioned in a previous post), in Germany
(, in UK
(, in France
(, etc., seem to
target attendees mainly interested in a different technolgical
cheminformation, closer to the one mentioned in case 1 by Xueshan Yan.
It seems to me that the two respective scopes of these two classes of
conferences have a reduced intersection.
Nevertheless, none of them should be ignored.
Regarding cases 2 and 3 mentioned by Xueshan Yan, I would like to read
more from FISers before commenting.

Thanks also to Robin Faichney for the example of information in
physics, that I would comment a bit (not joking).
I can understand that a two states system such as a spin can be viewed
as carrying a bit of information.
This is a good example of application of information theory to a
physical system. This class of examples is nice because it takes
benefit from the rigorous definitions available in the field, which
can be found in textbooks (Cover, Renyi, etc.).
However, since we assumed that information theory is a subfield of
information science (in addition to be a subfield of probability
theory), we also need very simple examples of information outside the
field of information theory.

Best regards,


2011/9/24 Xueshan Yan
 Dear Michel,

 It is very interesting for you telling us so many stories about the study of
 chemical information which took place in France and your university.

 As an information researcher, I once was invited to deliver a speech on
 Information Science at a meeting about chmoinformatics here a few years ago;
 I found their interests are far different from mine. Their main concerns are
 what information technology can be applied to chemistry――It seems as if you
 like this one according to your introductory post.But what we are eager to
 know is where the chemical information exists and how it functions between
 two molecules or supermolecules. As a matter of fact, I found there are
 three kinds of studies about information in chemistry.

 1. Chmoinformatics: A study about how to manage and compute chemical
 information, such as management of chemical abstracts, retrieval of chemical
 information through internet, molecules represented by graphs, data mining
 etc. there are many books like this in the bookstore. Of course, this may
 not be a subject that could arouse real interests among true information
 researchers, because there are thousands of applications of information
 technology in different areas, it is difficult for us to call all these
 applications of information technology as informatics or information

 2. Chmoinformatics: A study about how chemical information function between
 two molecules or two supermolecules, according to the terms in biology and
 chemistry: between substrate and receptor, or in coordination chemistry:
 between donor and acceptor, or host and guest, we can only consider this
 thought as a conjecture which proposed by Jean-Marie Lehn of University
 Louis Pasteur――the noble prize winner of 1987. As a matter of fact, we all
 know that in the process of molecule reaction and recognition, an
 intelligent is in esse. This has been proved by Fischer’s lock-and-key model
 early in 1894.

 3. Semiochemistry: A study about chemical information materials that mediate
 interactions between members of different species. This study consider
 pheromone, quinonyl compounds etc. as messengers. It is an interdiscipline
 of chemistry and biology.

 We especially want to know what advance about the second study about
 chemical information in chemists has made recent years. Because Lehn said in
 many places: “Supramolecular chemistry (chmoinformatics) has paved the way
 toward apprehending chemistry as an information science”.

 Best wishes,
 Xueshan Yan
 Peking University, FIS Beijing Group

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-23 Thread Michel Petitjean
Dear FISers,

Pedro raises several points.
Among them:

1. Chemoinformatics or Cheminformatics ?
Both terms are encountered. I would say that unless some authority
takes a decision, both terms will continue to be used.

2. Despite I gave an example of what could be cheminformation in a
concrete case, I did not tell what was exactly cheminformation in this
concrete case. I just asked the question of what it could be.
Now, I ask you the following: please can you provide an extremely
simple example (the most simple you could imagine) of situation in
which you can say:  in this situation, information is ... .
Chemical information is welcome, but an example from physics would be
great, too. However, please, no biology example, that will be dicussed
at the occasion of a future session.
These examples are expected to help us to define information in more
general situations.

3. The comparison Pedro did with symmetry is of interest: can anyone
define symmetry ?
During a long time, symmetry had in common with information that many
people attempted to define it in its own field, giving raise to many
particular definitions, but not to a common and widely accepted one.
Some years ago, although I needed to mention a definition of symmetry
in one of my papers, I was surprised that I could not find an unifying
one (symmetry is known since millenaries!!). Even in the book of Weyl
I did not find the expected one.
So, I decided to build my own one (Symmetry: Culture and Science,
2007, 18[2-3], 99-119; free reprint at See also:
In fact, the group structure which is generally a priori imposed, is a
consequence of several properties that the definition should satisfy
to be in agreement with some obvious intuitive requirements (and so,
five different groups appear naturally, none of them being imposed a
priori). Of course, the proposed unifying definition applies to a
broad spectrum of situations, not only the geometric one: matrices,
functions, distributions, graphs, etc.
But that was possible because I already had knowledge of the many
definitions in particular domains or situations.

Thus I expect that that you will post several examples of information
in very simples cases.
From the analysis of these situations we should move forward.

E.g., for symmetry, one of the simple examples I gave was the set of
three points of the real line: if one point is the mid of the two
other, there is symmetry (in fact, it is a case of achirality, i.e.
indirect symmetry, because here we deal with reflections rather than
with rotations).
It would be great to have so simple situations for information in
chemistry or physics.

Thanks by advance,
ll my best,


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-18 Thread Michel Petitjean
Dear Stan,
I would not insert an 'organic realm' in the hierarchy: it is part of
the chemical realm, but it is broader than expected.
The rules of Organic Chemistry are not universal as the theorems of
mathematics are: many exceptions exist, at least due to the existence
of multifunctional compounds. Even increasing the length of an alkyl
chain can give surprising results. It is why patents covering
syntheses of an infinite number of compounds should never have been
accepted, although they were. At the occasion of a course, we learned
the main rules needed to face to the realm of Organic Chemistry, but
the complexity of structural formulas we face (often natural products)
is incredibly vast, and each year we discover more. In parallel,
Organic Chemists establish new syntheses and reactions, and the
catalog of rules we have is now too large to be likely known by only
one Organic Chemist.
But compared to Biology, even Organic Chemistry remains simple !!
It means that we are as the midge trying to understand a computer: it
is unlikely that we will be successful.
But the challenge is so exciting, and we can take benefits from any
increase of knowledge.

2011/9/17 Stanley N Salthe
 Michel -- Organic chemistry was known to be the most difficult course in
 Columbia University.  But I got interested in it, worked very hard
 constantly, and I achieved an  'A'.  But what you say here indicates several
 orders of magnitude more difficulty than what I played with in university.
  For me this raises a question about the 'realms of nature', as in the
 subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
  Do you think one should place an 'organic realm' between chemical and
 biological?  Or, otherwise, do you think it possible that there might be
 organic realms out in the universe not entrained into biology?

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-17 Thread Michel Petitjean
Dear Joe, dear FISErs,

An organic chemist is able to predict a number of properties from the
structural formula, including much about reactivity of the compound.
But as you know, doing that properly is extremely difficult in a
number of cases, because the rules governing reactivity are much more
complicated that the ones which are taught at Universities, and the
number of rules expands rapidly each year. In fact, an experienced
Organic Chemist has in his head a so extraordinary rich collection of
rules and a so enormous knowledge that even many chemists which are
not Organicians cannot imagine the extent of this knowledge.
It is clear that the doing chemistry process derives from these
rules (these rules are chemical information), not only from the
Since the 70's, some cheminformaticians tried to store that in
databases: reactions databases plus databases of reactivity rules for
computer sssisted synthesis or retrosynthesis, etc., then built
programmes intended to output proposals supposed to help the chemist.
As far as I know, the brain of the Organician is still by far much
more efficient than the best softwares which were produced.
So, I may tell that the information available in the brain of the
Organician is extremely difficult to store on computer, and it is even
very difficult to teach it, apart the very beginning.
There are examples other than reactivity. A huge of QSAR studies were
done in order to predict various physico-chemical properties of simple
chemical compounds, e.g., predicting from the structural formulas the
boiling temperatures of monofunctional compounds such as alcohols,
cetones, etc. at 20 C under 1 atm. But even in these apparently simple
cases, the chemical information we need to do that with an acceptable
accuracy is difficult to extract: the conclusions of such QSAR studies
cannot be applied to any alcohol or cetone (still assumed to be
monofunctional compounds), and it is even difficult to know the extent
of validity of the published empirical rules, concretely often
summarized by some regression coefficients.
The example of spectroscopic databases is also of interest. How
simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
compounds ? Starting from the structural formula, it is really hard to
simulate, e.g. a low resolution mass spectra. Most time, it was
attempted to extract rules from spectroscopic databases, then try to
predict the spectra of a compound absent from the database, or
conversely, retrieving the structural formula of a compound from its
spectra(s). Many such softwares were developped since the 70's (one of
the oldest ones is STIRS), but really the chemical information needed
to do that properly is very difficult to extract.
To conclude, I retain your example of crystallization: for sure when
we will able to retrieve from the structural formula H-O-H that water
under 1 atm should crystallize at 0 C, then for sure we will be ready
to predict more about crystallization of chemicals.

Best regards,


 Dear Michel and FIS Colleagues,

 This will be an interesting discussion, since the core nature and role of
 information will be involved. Here is just one first point: to me, as a
 chemist, chemical information is only secondarily an object capable of
 being formalized, archived, etc. A formula has meaning for me in terms
 of the potential reactions the molecule to which it refers can undergo, what
 it looked like when crystallized for the first time and so on.

 Cheminformatics seems not to deal with such aspects of chemical information
 as part of a process of doing chemistry. Can this be captured by  another 

 Best wishes,


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[Fis] Chemical information: a field of fuzzy contours ?

2011-09-16 Thread Michel Petitjean
 the content of these records really meant.

For those who are unexperienced with databases in general, I consider
one of the simplest examples commonly encountered:
build a directory of names, say, of some colleagues. But some women
have two names, some people have surnames
(the first name/family name structure is culture and country
dependant), Russian people may have various English translations of
their name,
Chinese people too, etc. If you add to that the physical addresses,
building the directory can be a real nightmare:
did it happen that you were unhappy with a form in which your own data
cannot fit with what was expected ? Probably yes.
When the computerized database is read, it is clear that its content
should be understood at the information level:
what meant exactly each field of an entry in the directory. Without
this understanding, wrong conclusions can be
derived when reading the entries, and complex information to be
extracted can be biased, if not erroneous.
Now imagine the difficulties with complex databases such as structural
chemical databases !
Remark: once the data recorded in the database, you can reformat the
database as many times you like,
but it is too late to change the meaning of its content: this latter
should be carefully thought before recording any data.
Building and updating a database is generally expensive, and deciding
about the meaning of its content to be stored is a crucial step.
Alas, ambiguities and problems are often too late discovered.
I may say that focussing on formatting and structure of databases is
part of computer sciences,
although focussing on the meaning of what is stored is rather part of
information science.

Now we return back to chemistry. Cheminformatics is related to
chemical databases, and chemical information is to be extracted from
these databases.
Recall that information is not to be confused with data, and that
extracting information from data can be complex, but not always.
I would just mention one example of what could be considered to be a
chemical information, and that I called the parity phenomenon.
In 1990, I published in J. Chem. Inf. Comput. Sci. the distribution of
the number of carbons per compound in a database
of 3.424.428 compounds. This database contained most compounds
recorded by CAS until July 1978.
It appeared that the even values were systematically preferred to
the odd values
In fact it is not due to a coherent action of all chemists over the
world: the main part of the explanation
(published in the 1990 paper) relies on graph theory, although the
database emerged from the human activities.
In 1996 and 1997, the phenomenon was rediscovered in the Belstein
database, giving raise to four notes in Nature,
none of them mentioning the explanation (the original 1990 paper was not cited).
Here comes my question: in the example above, is the chemical
information the parity phenomenon by itself,
or is the chemical information its explanation, or is it something else ?
Anyway, this chemical information emerged from the chemical database,
and couldn't be retrieved without it.

Chemical information science is a subfield of information science
dealing with molecules,
and there is a close relation of information science(s) with
databases, in general. If not, where is information ?
May be in our head, and not only it can be communicated (e.g.,
teaching), but also it can be stored (not trivial to do properly).
During centuries it was stored in books. Now, it is in computer
databases, giving us a faster access to an enormous richness.
We just need people and time to investigate all that: an exciting task !

All web sites cited in the text above were accessed the 12 September 2011.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: (preferred),

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[Fis] The Assymetry of Information

2009-11-12 Thread Michel Petitjean
Faith in religion, faith in science, faith in information media, etc.
But let us consider that in a rough chronological order:

- Millenaries ago and still now: what is written is true because it is written
(well, some milenaries ago most people were unable to read)
- It is written in a book so it is true
- It is written in a journal so it is true
- It is heard at the radio, so it is true
- It is seen at tv so it is true
- The computer said that it is true, so it is true
- It is written in a web page so it is true
- It is written in Wikipedia so it is true
- It is written in a high rank science journal so it is true
- It is told by some VIP (very important politician) so it is true
- It is told by my director so it is true
etc. etc.
Yes we receive information. But received informations are most time
The asymmetry between the sender and the receiver is clear,
just as is clear the asymmetry between the vendor of something you
don't need and you:
the vendor needs your money, and it is why he delivers his information.
It is rarely good for you.
Information is received ? The question is: why the sender indeed sent
information ?

Michel Petitjean,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: +331 6908 4007
E-mail:, (preferred)
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[Fis] Symmetry Festival 2009 / 2-nd circular

2009-02-10 Thread Michel Petitjean
Dear FISers,

The Symmetry Festival 2009 will be held in Budapest, 31 July - 4 August.
The deadline for abstract submission is: 15 February 2009.

The Conference is transdisciplinary: maths, science, education, art.
Please visit the site:

FIS is also transdisciplinary, and the fields of Information and
Symmetry have much in common.

Proceedings: accepted papers will be published in the Journal
Symmetry: Culture and Science (ISSN 0865-4824).
The anonymous peer review process applies.

Provisional list of speakers:

Steven Weinberg (The University of Texas at Austin, USA)

Michele Emmer (Sapienza Universita di Roma, Italy)
Chaim Goodman-Strauss (University of Arkansas, USA)
Dezso Horvath (KFKI RMKI, Hungary and LHC CERN, Switzerland)
Alajos Kalman (Chemical Research Center, Hungary)
Gabor Naray-Szabo (Eotvos Lorand University, Hungary)
Meir Shinitzky (Weizmann Institute of Science, Israel)
Tibor Toro (Sapientia University, Romania)

Planned special sessions:

# Symmetry in the history and philosophy of science
# Symmetry in the history of interdisciplinary approaches in the sciences
# Symmetry in the history of physics, chemistry and material science
# Symmetry in the history of mathematics
# Arts and the space research (application of symmetry considerations)
# Symmetry in life sciences, medicine and pharmacology
# Symmetry as a medium between the arts and the sciences
# Symmetry principles in architecture and design
# Origami in science and art
# Symmetries and visualisation
# Symmetry in bioinformatics
# Symmetry in Linguistics
# Education and symmetry

I hope to meet you in Budapest!

Best regards,


Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: +331 6908 4007
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[Fis] information(s)

2008-12-06 Thread Michel PETITJEAN
Hello FISers.

Recently, one of my colleagues attract my attention on the following point.
In French, we often use information as a countable quantity,
so that we can write informations.
In English, it seems that it is unusual, if not incorrect, to do that.
(1) Please can some English native FISers give their opinion about that ?
(2) Please can some FISers from non English-speaking countries tell us
how is the situation in their own language ?

Thank you very much.


Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: +331 6908 4007

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[Fis] Symmetry thematic issues / call for papers

2008-10-22 Thread Michel PETITJEAN

To: recipient list suppressed
Subj: Symmetry thematic issues / call for papers

/* Apologies for unwanted or multiple receipts */

Dear Colleague,

The Journal Symmetry: Culture and Science, ISSN 0865-4824,
is running several thematic issues:

Symmetry in Nanostructures
Guest Editor: Mircea V. Diudea ([EMAIL PROTECTED])

Guest Editors: Michel-Marie Deza ([EMAIL PROTECTED]) and Egon Schulte ([EMAIL 

Symmetry in Literature
Guest Editor: Tatiana Bonch-Osmolovskaya ([EMAIL PROTECTED], [EMAIL PROTECTED])

Symmetry in Mathematical Education
Guest Editor: Raymond Tennant ([EMAIL PROTECTED])

Islamic Art and Symmetry
Guest Editor: Raymond Tennant ([EMAIL PROTECTED])

You are kindly invited to contribute (paper, review, short note).
Please visit the Journal website:
or contact the appropriate Guest Editors for any further information.

Other event: Symmetry Festival 2009 (Budapest, 31 July - 4 August)
Deadlines, etc.:
Proceedings: accepted papers will be published in the journal Symmetry: 
Culture and Science.

Thank you very much.
Best regards,
Michel Petitjean, Editor-in-Chief

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[Fis] Symmetry Festival 2009 / First circular

2008-10-18 Thread Michel PETITJEAN

To: recipient-list suppressed
Subj: Symmetry Festival 2009 / First circular

Dear Colleague,

I am very pleased to inform you that the Symmetry Festival 2009
will be held in Budapest, 31 July - 4 August.

The Conference is transdisciplinary: maths, science, education, art.
Please visit the site:

Proceedings: accepted papers will be published in the Journal
Symmetry: Culture and Science (ISSN 0865-4824).

More information: please contact the Conference Chair:
Prof. Gyorgy Darvas ([EMAIL PROTECTED]).

Best regards,

Michel Petitjean, Editor-in-Chief of Symmetry, ISSN 0865-4824
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: +331 6908 4007

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[Fis] Journal call for papers (ISSN 0865-4824)

2008-01-12 Thread Michel Petitjean
To: recipient-list suppressed
Subj: Journal call for papers (ISSN 0865-4824)

/* Apologies for unwanted or multiple receipts */

Dear Colleague:

The Journal Symmetry: Culture and Science (ISSN 0865-4824)
launches thematic issues on the following topics:

* Symmetry in Mathematical Education
Guest Editor: Raymond Tennant ([EMAIL PROTECTED])

* Islamic Art and Symmetry
Guest Editor: Raymond Tennant ([EMAIL PROTECTED])

* Symmetry in Literature
Guest Editor: Tatiana Bonch-Osmolovskaya ([EMAIL PROTECTED], [EMAIL PROTECTED])

* Symmetry and Entropy
Guest Editors: Marlos Viana ([EMAIL PROTECTED]) and Julio Stern ([EMAIL 

Your contributions are welcome (to be submitted directly to the Guest Editors).

Please feel free to publicize this announcement.

Thank you very much.

Michel Petitjean, Editor-in-Chief.
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